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Glossary – Terminal SNP

The phrase Terminal SNP is generally used in conjunction with discussing Y DNA testing and haplogroup identification.

SNPs Define Haplogroups

In a nutshell, SNPs, single nucleotide polymorphisms, are the mutations that define different haplogroups. Haplogroups reach far back in time on the direct paternal, generally the surname, line.

SNPs, mutations that define haplogroups are considered to be “once in the lifetime of mankind” events that divide one haplogroup into two subgroups, or branches.

A haplogroup can be thought of as the ancient genetic clan of males – specifically their Y DNA. You might want to read the article, What is a Haplogroup?

If you test your Y DNA with Family Tree DNA, you’ll notice that you receive an estimated haplogroup with the regular Y DNA tests which test STR, or short tandem repeat, markers. STRs are the markers tested in the 37, 67 or 111 marker tests. You can read about the difference between STRs and SNPs in the article, STRs vs SNPs, Multiple DNA Personalities.

STR markers are used for more recent genealogical testing and comparison, while haplogroups reach further back in time.

An estimated haplogroup as provided by Family Tree DNA is based on STR matches to people who have done SNP testing. Estimated haplogroups are quite accurate, as far as they go. However, by necessity, they aren’t deep haplogroups, meaning they aren’t the leaves on the end of the twigs of the branch of your haplotree. Estimated haplogroups are the big branches.

In essence, what a haplogroup provided with STR testing tells you is the name of the town and the main street through town. To get to your house, you may need to turn on a few side streets.

Haplotree

The haplotree, back in the ancient days of 2002 used to hold less than 100 haplogroups, each main branch called by a different letter of the alphabet. The main branches or what is referred to as the core backbone is shown in this graphic from Wikipedia.

Today, the haplotree shown for each Y DNA tester on their personal page at Family Tree DNA, has tens of thousands of branches. No, that’s not a misprint.

The haplotree is the phylogenetic tree that defines all of the branches of mankind and groups them into increasingly refined “clans” or groups, the further down the tree you go.

In other words, Y Adam is at the root, then his “sons” who, due to specific mutations, formed different base haplogroups. As more mutations occurred in the son’s descendants’ lines, more haplogroups were born. Multiply that over tens of thousands of years, and you have lots of branches and twigs and even leaves on the branches of this tree of humanity.

Let’s look at the terminal SNP of my cousin, John, on his Haplotree and SNP page at Family Tree DNA.

John’s terminal SNP is R-BY490. R indicates the main branch and BY490 is the name of the SNP that is the further down the tree – his leaf, for lack of a better definition.

In John’s case, we know this is the smallest leaf on his branch, because he took the Big Y test which reads all of his SNPs on the Y chromosome.

Haplogroup R is quite large with thousands of branches and leaves – each one with its own distinct history that is an important part of your genealogy. Tracking where and when these mutations happened tells you the migration history of your paternal ancestor.

How else would you ever know?

How Do I Discover My Terminal SNP?

Sometimes “terminal SNP” is used to mean the SNP for which a man has most recently tested. It may NOT mean that he has tested for all of the available SNPs. What this really means is that when someone gives you a terminal SNP name, or you see one listed someplace, you’ll need to ask about the depth of the testing undergone by the man in question.

Let’s look at an example.

I’ve condensed John’s tree into only the SNPs for which he tested positive. The entire tree includes SNPs that John tested negative for, and their branches which are not relevant to John – although we certainly didn’t know that they weren’t relevant before he tested. However, he may want to reference the large and accurate scientific tree, so all information is provided to John. It’s like seeing a map that includes all roads, not just the one you’re traveling.

I’ve created a descendant chart style tree below. Y line Adam is the first male. Some several thousands of years later, his descendant had a mutation that created haplogroup R defined by the SNP M207, in yellow.

John, based on his STR matches, was predicted to be R-M269. On his results page, that’s the estimated haplogroup that was showing when his results were first returned.

If you had asked John about his terminal SNP, he would have probably told you R-M269. At that time, to the best of his knowledge, that WAS his terminal SNP – but it wasn’t really.

John could choose three ways to test for additional SNPs to discover his actual terminal SNP.

One by One

John could selectively test one SNP at a time to see if he was positive, meaning that he has that mutation. SNPs cost $39 each to test, as of the time this article was written. Of course, John could also be negative for that SNP, meaning he doesn’t have the SNP, and therefore does not descend from that line. That’s good information too, but then John would have to select another branch to test by purchasing the SNP associated with that new branch.

If John had selected any of the SNPs on the list above to test, he would have tested positive. So, let’s say John decided to test L21, a major branch. If he tested positive, that means that all of the branches directly above L21, between L21 and M207, are also positive, by inference.

At that point, John would tell you that his terminal SNP is L21, but it isn’t actually.

SNP Packs

Now, John wants to purchase a more cost-effective SNP pack, because he can test 100 or more SNP locations by purchasing one SNP pack for $99. That’s a great value, so John purchases the SNP pack offered on his personal page. A SNP pack tests selective SNPs all over the relevant portion of the tree in an attempt to place a man on a relatively low branch. These SNPs are selected to find an appropriate branch, not the appropriate leaf. They confirm (or disprove) SNPs that have already been discovered.

Let’s say, in John’s case, the SNP pack moves him down to R-ZP21. If you asked him now about his terminal SNP, he would probably tell you R-ZP21, but it still isn’t actually.

SNP packs are great and do move people down the tree, but the only way to move to the end of the twigs is the Big Y test.

The Big Y Test

The Big Y test tests for all known SNPs as well as what were called Novel Variants and are now called Unnamed Variants which are new SNPs discovered that are as yet unnamed. You may have a new SNP in your line waiting to be discovered. The Estes family has one dating from sometime before 1495 that, to date, has only been found in Estes descendant males from that common ancestor who was born in 1495.

The Big Y test, at $575, scans virtually the entire Y chromosome in order to place testers on the lowest leaf of the tree. You can’t get there any other way with certainty and you’ll never know if you have any as yet undiscovered SNPs or leaves unless you take the Big Y.

In John’s case, that leaf was 4 more branches below R-ZP21, at R-BY490.

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Why Does a Terminal SNP Matter?

Haplogroup R-M269 is the most common haplogroup of European men.

Looking at the SNP map, you can see that there are so many map locations as to color the map of the UK entirely red.

Genealogically, this isn’t helpful at all.

However, looking now at DF49, below, we see many fewer locations, suggesting perhaps that men with this terminal SNP are clustered in particular areas.

SNPS further down John’s personal haplotree tell an increasingly focused and granular story, each step moving closer in time.

Summary

Men generally want to discover their terminal SNP with the hope that they can learn something interesting about the migration of their ancestors before the genesis of surnames.

Perhaps they will discover that they match all men with McSurnames, suggesting perhaps a Scottish origin. Or maybe their terminal SNP is only found in a mountainous region of Germany, or perhaps their Big Y matches all have patronymic surnames from Scandinavia.

Big Y testing is also a community sourced citizen science effort to expand the Y haplotree – and quite successfully. The vast majority of SNPs on the publicly available ISOGG Y tree today are from individual testers, not from academic studies.

Haplogroups, and therefore terminal SNPs are the only way we have to peek back behind the veil of time.

If you’re interested in discovering your terminal SNP, you’ll be money ahead to simply purchase the Big Y up front and skip individual SNP testing along with SNP packs. In addition to discovering your terminal SNP, you are also matched to other men who have taken the Big Y test.

You can order the Big Y, individual SNPs or SNP packs by clicking on this link, signing on to your account, and then clicking on the blue “Upgrade” button, either in the Y DNA section, shown below, or in the upper right hand corner of your personal page.

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Nice review of this subject. I am not disagreeing with your recommendation in the next to last paragraph to just purchase the Big Y test, but when I first got my Y-DNA results back in 2008, I used Whit Athey’s Haplogroup predictor (http://www.hprg.com/hapest5/) and it predicted that I should be I-L38 to 98% probability. Based on that I ordered the FTDNA’s I-L39 SNP test (equivalent to I-L38) and it confirmed that result – not bad for a $39 test.

The terminal SNPs and the SNP packs do a good job of confirming existing SNPs, but if you want to find out if you have any SNPS that have not yet been discovered, or you want to find your most refined SNP, the Big Y is the only way to do that. Generally, the Big Y is only needed for one man in a family group, because all other men from that same line will match him, or within one SNP.

More recently I ordered the SNP pack recommended for the I-L38 project at FTDNA and that took me down to I-FGC36962. I also ordered the Big Y in this last sale. It will be interesting to see what that brings.

By moving down 15 branches, was the BY490/Big-Y test results able to provide a more precise geographical results. I notice that the RM269 map was spread out all over Europe and DF49 narrowed down the geographical results to the United Kingdom. So does the BY490 narrow down the geographical suggestion even further? Thanks, Vic V.

Gosh yes. Each “click” further down the tree generally has that effect, although some may have too few to register on the map today. You do ask a good question though, and it sounds like a good blog article.

Ah, I was looking for it in the BigY section, not the Y-DNA section. It’s been almost 4 years since I did my Y-DNA111 test and the SNP map wasn’t there back then. I guess I missed when they added it and haven’t noticed it since then.

Shame on promoting the term terminal SNP. It is NOT terminal in that it can, and will change, as new results are acquired. By definition terminal is not something that changes. It is more appropriate to state that they are the most recently shared variant.

For genealogical purposes it is best to have MULTIPLE results from individuals in the family line. Start out with results from 5th+ cousins. Remember that this allows one to define the appearance and location of the most recently shared variant within genealogical time. More and more families are working their brick walls using full y-chromosome results. Individuals going with higher resolution test results, such 20x+ whole genome, will end up with more genealogically relevant variants than someone who tests with BigY.

Terminal SNP is the term used. I didn’t create that term. Furthermore, the SNP itself doesn’t change. We discover SNPs further down the tree. One your terminal SNP has been identified, you don’t obtain a new one. Whole genome sequencing isn’t going to affect the Y chromosome SNPs. We are already reading the stable region from he Y today.

Thanks for your clear explanation. However, I still have some doubts, as I got my BigY results yesterday:
My haplotree says “your confirmed haplogroup is:E-CTS1096” (which hasn’t changed since I imported my results from Geno 2.0). However, down the tree it says E-S11956 (marked in green), and below that, it still offers me individual SNP tests.
On Ytree, it looks like E-CTS1096 and E-S11956 are the same thing.., and that would mean I didn’t move any step down with the bigY.
Am I wrong or missing something?

But for those R-M269ers where the Big Y is currently out of reach ($) which is better adding/upgrading STR or adding a SNP Pack? Or should I say in which situations is adding STR more useful than SNP Pack or vice versa?

Example: Tested at Y-37 resulted in R-M269. Zero matches with same surname or anything close to it. Very few matches with earliest ancestor in the same known country of origin as mine. (But of course most give no indication of location at all.) 6 matches at Y-37 all at Genetic Distance 4, 1,486 at Y-25 (six at Genetic Distance 0) and 2,667 at Y-12.

Of the six matches at Y-37 four tested at 67, one at 111 and the last gives no information of tested level. Of those six two are not on the same continent and four give no location whatsoever. But based on surname of tested persons they are likely not from same country.

My purpose of testing was to learn the Y Haplogroup and save/bank it so I have a tested person from my line that eventually if I can get someone to test I can compare to a direct male from each of the two other family groups of the same name who came to the same county whose origins are all six miles apart from each other in three small villages. (No “paper” church documents currently found here or there link the three family groups together as one despite their closeness but none exist saying not related either.)

Can’t decide which situation is better: the most common European Y-Haplogroup with lots of matches beyond genealogical time or a unique mt-Haplogroup with absolutely zero matches. Best and Worst in both worlds?

Hi, Roberta,
My brother took the 23andme test and he got R-L23 which is too broad to be useful. I know they do the bare minimum. However, when I had it analyzed via the Chris Morley tool, he ended up with was negative for M412/L62/PF6536/S167. Do you have any suggestions about what test he should take to further breakdown his results?

Given the pricing at Family Tree DNA right now, I’d suggest that he order the minimum Y STR test and then the Big Y upgrade and receive the discounted pricing to find your very most specific haplogroup.

We utilized genealogy records from England, and then we created a pedigree chart utilizing those records and SNP data from the men we tested. The two worked in tandem. We were very very fortunate to find a man from a very early ancestor through another son.